TY - JOUR
T1 - Rb×1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation
AU - Liu, Jin
AU - Nussinov, Ruth
N1 - Funding Information:
This project was funded in whole or in part by federal funds from the National Cancer Institute, National Institutes of Health (NIH), under contract number HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. Support was also provided by the Intramural Research Program of the Center for Cancer Research, National Cancer Institute, NIH. This study used the high-performance computational capabilities of the Biowulf Linux cluster at the NIH, Bethesda, MD ( http://biowulf.nih.gov ).
PY - 2010/8/4
Y1 - 2010/8/4
N2 - In ubiquitination, cullin-RING E3 ubiquitin ligases (CRLs) assist in ubiquitin transfer from ubiquitin-conjugating enzyme E2 to the substrate. Neddylation, which involves NEDD8 transfer from E2 to E3-cullin, stimulates ubiquitination by inducing conformational change in CRLs. However, deneddylation, which removes NEDD8 from cullin, does not suppress ubiquitination in vivo, raising the question of how neddylation/deneddylation exerts its effects. Using molecular-dynamics simulations, we demonstrate that before neddylation occurs, the linker flexibility of Rb×1, a CRL component, leads to conformational changes in CRLs that allow neddylation and initiation of ubiquitination. These large NEDD8-induced conformational changes are retained after deneddylation, allowing both initiation of the ubiquitination process and ubiquitin chain elongation after deneddylation. Furthermore, mutation of lysine, the cullin residue to which NEDD8 covalently attaches, dramatically reduces CRL conformational changes, suggesting that the acceptor lysine allosterically regulates CRLs. Thus, our results imply that neddylation stimulates ubiquitination by CRL conformational control via lysine modification.
AB - In ubiquitination, cullin-RING E3 ubiquitin ligases (CRLs) assist in ubiquitin transfer from ubiquitin-conjugating enzyme E2 to the substrate. Neddylation, which involves NEDD8 transfer from E2 to E3-cullin, stimulates ubiquitination by inducing conformational change in CRLs. However, deneddylation, which removes NEDD8 from cullin, does not suppress ubiquitination in vivo, raising the question of how neddylation/deneddylation exerts its effects. Using molecular-dynamics simulations, we demonstrate that before neddylation occurs, the linker flexibility of Rb×1, a CRL component, leads to conformational changes in CRLs that allow neddylation and initiation of ubiquitination. These large NEDD8-induced conformational changes are retained after deneddylation, allowing both initiation of the ubiquitination process and ubiquitin chain elongation after deneddylation. Furthermore, mutation of lysine, the cullin residue to which NEDD8 covalently attaches, dramatically reduces CRL conformational changes, suggesting that the acceptor lysine allosterically regulates CRLs. Thus, our results imply that neddylation stimulates ubiquitination by CRL conformational control via lysine modification.
UR - http://www.scopus.com/inward/record.url?scp=77955682724&partnerID=8YFLogxK
U2 - 10.1016/j.bpj.2010.05.021
DO - 10.1016/j.bpj.2010.05.021
M3 - Article
C2 - 20682250
AN - SCOPUS:77955682724
SN - 0006-3495
VL - 99
SP - 736
EP - 744
JO - Biophysical Journal
JF - Biophysical Journal
IS - 3
ER -